Coho, Jack Coho, and Steelhead passages at the Willamette Falls
This report analyzes fish passage data at Willamette Falls from the University of Washington’s Columbia Basin Research initiative. The ongoing, collaborative data collection by federal, state, and tribal agencies examines passages of several fish species at the passage ladder. This analysis visualizes time-series data from 2001 to 2010 of Coho, Jack Coho, and Steelhead
Willamette Falls is located in Oregon’s Willamette Valley, as seen below:
# image
include_graphics(here("_posts", "2022-03-11-willamette-falls", "data", "willamette_falls.jpg"))
Source: Willamette Valley Heritage
The fish ladder is located near the falls:
# image
include_graphics(here("_posts", "2022-03-11-willamette-falls", "data", "fish_ladder.jpg"))
Source: US Army Corps of Engineers
Data Citation: University of Washington, Columbia Basin Research. 2010. DART Adult Passage Graphics & Text. http://www.cbr.washington.edu/dart/query/adult_graph_text.
We will use various seasonal plots to examine fish passages for Coho, Jack Coho, and Steelhead over the ten year period.
fish_ts <- fish %>%
as_tsibble(key = NULL, index = date) %>%
select(coho, jack_coho, steelhead) %>%
replace_na(list(coho = 0, jack_coho = 0, steehlead = 0)) %>%
pivot_longer(cols = c(coho, jack_coho, steelhead),
names_to = "fish_spp",
values_to = "passage_count") %>%
mutate(fish_spp = case_when(fish_spp == "coho" ~ "Coho",
fish_spp == "jack_coho" ~ "Jack Coho",
fish_spp == "steelhead" ~ "Steelhead"))
hchart(fish_ts,
"line",
hcaes(x = date, y = passage_count, group = fish_spp),
color = c("#b5c7ab", "#ffbdbd", "#c9c9ff")) %>%
hc_title(
text = "Daily Counts of Fish Species") %>%
hc_xAxis(
title = list(text = "Date")) %>%
hc_yAxis(
title = list(text = "Passage Count"),
min = 0) %>%
hc_caption(
text = "<b>Figure 1.</b> Time series of fish passage counts for Coho, Jack Coho, and Steelhead at Willamette Falls from 2001 to 2010",
useHTML = T)
All 3 fish species observed at consistent seasonal intervals at Willamette Falls
Coho and Jack Coho observed passing through Willamette Falls at the same time while Steelhead pass in the opposite seasons
Coho passages steadily increase and peak around 2011
Jack Coho have smallest number of observations with no apparent trend for count changes over time
fish_month <- fish_ts %>%
pivot_wider(names_from = fish_spp,
values_from = passage_count) %>%
index_by(yr_mo = ~yearmonth(.)) %>%
summarize(monthly_mean_steelhead = mean(Steelhead, na.rm = TRUE),
monthly_mean_coho = mean(Coho, na.rm = TRUE),
monthly_mean_jack_coho = mean(`Jack Coho`, na.rm = TRUE))
steelhead_season <- fish_month %>%
gg_season(y = monthly_mean_steelhead,
pal = paletteer_c(palette = "ggthemes::Classic Red-Green Light", n = 10)) +
labs(x = "Month", y = "Steelhead") +
theme_minimal() +
theme(legend.position = "none")
coho_season <- fish_month %>%
gg_season(y = monthly_mean_coho,
pal = paletteer_c(palette = "ggthemes::Classic Red-Green Light", n = 10)) +
labs(x = " ", y = "Coho") +
theme_minimal() +
theme(legend.position = "none") +
theme(axis.title.x = element_blank(),
axis.text.x = element_blank())
jack_season <- fish_month %>%
gg_season(y = monthly_mean_jack_coho,
pal = paletteer_c(palette = "ggthemes::Classic Red-Green Light", n = 10),
year.labels = TRUE,
continuous = TRUE) +
labs(x = " ", y = "Jack Coho") +
theme_minimal() +
theme(legend.position = "right") +
theme(axis.title.x = element_blank(),
axis.text.x = element_blank())
coho_season / jack_season / steelhead_season + plot_annotation("Daily passage of fish from 2001 to 2010", caption = "Figure 2. Seasonplot of fish species runs over the course of a year from 2001 to 2010 at the Wilamette Falls fish ladder.")
Coho and Jack Coho runs at the Willamette Falls ladder occur from August to November, concentrated in October
Steelhead runs at Willamette Falls occur almost exclusively in the months Coho and Jack Coho do not pass the ladder
fish_counts <- fish %>%
# as_tsibble(key = NULL, index = date) %>%
select(coho, jack_coho, steelhead, date) %>%
replace_na(list(coho = 0, jack_coho = 0, steelhead = 0)) %>%
pivot_longer(cols = c(coho, jack_coho, steelhead),
names_to = 'fish_species',
values_to = 'passage_count') %>%
mutate(fish_spp = case_when(fish_species == 'coho' ~ "Coho",
fish_species == 'jack_coho' ~ "Jack Coho",
fish_species == 'steelhead' ~ "Steelhead")) %>%
mutate(year = year(date)) %>%
select(-date) %>%
group_by(year, fish_spp) %>%
summarize(annual_counts = sum(passage_count)) %>%
pivot_wider(names_from = fish_spp, values_from = annual_counts)
fish_annual <- highchart() %>%
hc_xAxis(categories = fish_counts$year) %>%
hc_add_series(
name = "Coho", data = fish_counts$Coho, color = "#b5c7ab") %>%
hc_add_series(
name = "Jack Coho", data = fish_counts$`Jack Coho`, color = "#ffbdbd") %>%
hc_add_series(
name = "Steelhead", data = fish_counts$Steelhead, color = "#c9c9ff") %>%
hc_title(text = "Annual passages of fish") %>%
hc_xAxis(
title = list(text = "Year")) %>%
hc_yAxis(
title = list(text = "Passage Counts"),
min = 0) %>%
hc_caption(
text = "<b>Figure 3.</b> Annual passages of Coho, Jack Coho, and Steelhead at Willamette Falls from 2001 to 2010",
useHTML = T)
fish_annual
Steelhead are the largest fish population that pass through Willamette Falls every year until 2009, when Coho passages more than quintuple
Jack Coho exhibit the most stable passage observations and also the least number of passages
Steelhead had a downward trend and rebound after 2009
The fish ladder at Willamette Falls offers a unique opportunity to observe seasonal patterns of fish. In this report, I analyzed the seasonal patterns of passage through Willamette Falls for Coho, Jack Coho, and Steelhead fish. Several conclusions are apparent:
All 3 species exhibit consistent seasonal patterns of passage, with Coho and Jack Coho passing during the same season (fall) and Steelhead passages peaking in late spring
Steelhead passages have decreased over time with their minimum passages in 2009, followed by rebounding in 2010
Both Coho species have seen an increase in passage observations over the ten year period